Clean output directories per sample

[jasmezz]

Description of feature

We need to clean up some output directories where multiple files per sample need to be put in individual sample folders.
For example this:

is supposed to look like this:

This is currently necessary for:

• ampir
• gecco
• hamronization
• prodigal
• rgi
• prodigal

[jfy133]

Devils advocate: this isn't necessary, as we should standardise/summarise everything with hAMRronization/AMPcombi etc., so maybe it's better to leave the output as expected for the tool (so a user can follow output docs of the given tool)

[jasmezz]

I understand, not completely convinced though. With fARGene we are already doing it (it's just adding ${meta.id} to the modules.config). Because fARGene output would look completely messy without the subfolders. So either remove its ${meta.id} or add it to all tools?

[jasmezz]

Closed by #107.